He's gone
by x.Technochocolate.x
Summary: Tony has to get up early for a mission in New York and Pepper acts extremely secretive. Will Tony have the opportunity to find out what she's hiding from him? Read and Review please! :D(( I am terrible at summaries ))
1. Chapter 1

**_Authors Note: Hey there! Okay so, I really wanted to write this story. I've had the idea for a while now and I finally got the time to write it down. This is my first ever piece of fanfiction so don't hate me too much! I'm new at this! xD_**

**_Also English is not my home language so if there is any grammar / spelling errors just point them out and I'll be more than happy to fix them for you._**

**_I hope this story doesn't suck too bad. Please Review/Fave and I'll be sure to update if I have readers :P_**

**_Disclaimer: I just want to point out, nothing is mine and everything belongs to their rightful owners._**

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**Chapter 1:** Fashionably late.

_Pepper's POV_

I opened my eyes it was still extremely early in the morning but I had to wake Tony up. He had a mission today, personally given to him by Nick Fury and he needed to be in New York in 6 hours. And because we're talking about Tony here, Fury asked me to make sure he woke up and made it on time.

I stretched my arms out to feel the other side of the bed. Yep, just like I thought. Tony was still curled up in a ball, sleeping. I pulled myself to a sitting position and crawled closer to him.

"Tony, wake up."I whispered and gave him a gentle kiss on the cheek.

He pulled the blankets over his head and sighed."I don't wanna." He mumbled, barely audible.

I couldn't help but smile. "Tony you have a mission in New York and when you come home I'll have the biggest surprise for you...!"I grinned when I thought back on what I found out a short week ago.

He sat up and blinked. "Pepper, you can't tell me things like that... Now I'm going to be curious the entire day long!"He sighed, he was clearly awake now. "Please tell me."He whined and I laughed, he looked like a five year old begging to know what his birthday present was.

"No, I'll tell you after your mission."I grinned and he pouted.

"But Pepper! I won't be able to focus If you don't tell me! PLEASE!" He made his lip wobble and I pulled him in for a gentle kiss.

"Oh trust me Tony, you won't be able to focus **at all**, if I tell you now."I replied with my lips still pressed against his.

He mumbled something and stood up. "Fine! but as soon as I come back you **have **to tell me! Got it?" He narrowed his eyes playfully and I nodded.

"I promise." with that said he left to get ready.

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One hour later I sat in the kitchen, I had just finished making Tony some breakfast and he was **still **getting ready, I relaxed and read through the paper.

"Hey Pep!"I heard his voice behind me and smiled. "Something smells delicious!"He added as he gave me a soft kiss on the cheek.

"I made waffles, you're favorite!"I grinned and he pressed another kiss on my cheek.

"Wow! Thanks Pep! You're seriously the best thing in my life... ever!"He exclaimed as he dived into his stack of waffles.

"For now."I whispered and he raised an eyebrow.

"What does_ **that_ **mean?"He asked curiously while taking yet another bite.

I smirked and closed the paper. "I'll tell you when you get back..."

His facial expression turned both confused and curious... "PEPPER PLEASE TELL ME NOW!"He shouted with a full mouth and I smiled in accomplishment while standing up.

"No. You have to get going anyways Mr Stark."I smiled and he chuckled softly.

"Whatever you say Mrs **Stark**."He took the last bite of his waffles and joined me at the stairs. "You're probably right though...At this rate I'll be about 30 minutes late already."He grinned sheepishly.

"Fashionably late as always Tony."I reminded him and he nodded.

"I'm gonna go now, I'll see you tonight if everything goes well."He joked and I punched him in the arm.

"Don't even make jokes about that Tony!"I growled and punched him again.

He lifted his arms up in surrender and pulled me into a long passionate kiss.

"I promise I'll come back Pepper."He whispered in my ear and I nodded.

"You better."

He gave me one last gentle kiss before he began to walk down the stairs to his workshop and a few seconds later I heard him fly off.

"You're going to be such a great dad Tony."I whispered while looking out the window as his figure disappeared into the distance. Little did I know that, that would be the last time I'd see him.

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**So how was that? Please review! I might just upload another chapter later today if there is any interest. :D**

**Thanks for reading!**

**xxx**


	2. Chapter 2

**Authors note: Okay first of all! Thank you all so much for the reviews! :D So here is another chapter as promised and I hope you enjoy it! I would also just like to clear up something. Tony is not dead! o: Don't worry! He's just going to be.. uhmm absent for a while... Yeah lets put it like that ;P So anyways... Read and Review/Like.**

**Disclaimer: I own nothing, everything belongs to their rightful owners.**

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**Chapter 2: **Gone.

_Tony's POV_

As I flew to New York I couldn't help but let my mind drift to Pepper and how she's been acting the last few days. What is she keeping from me? And why doesn't she want to tell me until tonight. I mean really... I can't wait till then! I won't be able to focus at all today. I sighed. Whatever news she has must be something huge. I let my mind wander a little more on that until I got snapped back to reality when Jarvis spoke.

"Sir, Nick Fury is calling." The AI said.

"Answer Jarvis."I replied immediately."

"Of course sir."

Everything was silent for a few seconds until Nick Fury finally spoke. "Stark? Are you in New York yet?"He asked bluntly.

"Uh. Good to hear your voice to Fury!"I said sarcastically."And to answer your question, almost, so would you be so kind to tell me what I'm doing here exactly?" I asked.

"Stark. I'm pretty sure I already told you that when I gave you the mission and I'm also certain you agreed and accepted."He replied with a sigh.

"Uh-huh. I was probably just agreeing to everything you were saying so you'd shut up."I chuckled. "Nothing personal though, so would you maybe just give me a short summary?"

He just sighed."You have to do an area scan Stark. We have gotten reports of unknown activity in the area and we need you to go check it out and rule out the possibility of another alien invasion. So unless you want history to repeat itself. Get to it." He ordered.

"Seriously... I had to come all this way to do an area scan? Of a _possible _threat... Couldn't you have asked Barton to do it?"I asked a bit annoyed.

"Couldn't you of paid attention the first time I mentioned the mission."He replied calmly.

"Touché, eyepatch." I teased him. I really didn't like losing arguments. He stayed silent. "Well anyways Fury. I've been circling the area and I can't really find anything _threatening _so thank you so much for wasting my ti-" I was cut of by a sudden loud exploding noise behind me then a shockwave that blew me right out of the air. I fell back to the ground at a swift speed unable to stabilize myself on time.

I landed on my stomach and I'm sure if I hadn't had the suit on I'd probably be a red splash on the ground. A sharp pain shot through my entire body and I couldn't help but let an agonizing groan of pain escape my throat. I lie still while breathing rapidly. My ears were ringing like crazy. I couldn't hear. I couldn't move but I could feel the darkness slowly move over me. What exactly just happened? I thought as everything went black.

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_Nick Fury's POV_

"Stark shut up and do your damn jo-" That's when I heard the explosion through the speaker followed by Stark's suit colliding with the ground. "Stark? What's happening?"I asked concerned when I heard another crash that lead to the line going static."Stark?"

I turned to Agent Hill who had been by my side the entire time. "Agent! Send out other agents to Starks last location, something is not right! I'll get Barton and Romanoff"

"Yes sir!"She obeyed and sprinted off.

I immediately tried reaching agent Barton and was surprised when he ran in through my door. "I was on my way to you when Agent Hill ran passed me and told me something happened to Stark?"He said as he entered. "I let Natasha know, she's on her way. Just give me the details and we'll go check things out."He added completely taking over the conversation.

I gave him the location and the rest of the important details and he was off once again."Keep me updated!"I shouted after him.

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_Clint Barton's POV_

I met Natasha at the helicopter we were going to use to fly out and search for Stark. We were quite a long distance away but managed to get there in just a short half hour. We were also pleased to discover the explosion wasn't near any civilization.

Natasha landed the helicopter a short distance away from the blast site and we jumped out in search for Stark or anything suspicious.

"Any luck Tasha?"I asked after a few minutes of searching.

She sighed. "No, there's no sign of Stark anywhere... As a matter of fact. There's no sign of anyone or anything that might of caused this..."She added confused. "Call director Fury... Tell him whoever did this intended to get Stark and Stark only."She added looking me straight in the eye. "They took him Clint."

I let my eyes drift to the ground before I called Fury to let him know.

"You're sure he's not there?"Fury asked with a sigh.

"Yeah... Pretty sure... No sign of him or anyone." I replied. "We're on our way back to you. I think it's time to assemble the rest of the team. So you should call Rogers and Banner and maybe try to get a hold of Thor if that's even possible. So see you soon."I added and ended the call.

We walked back to our helicopter and just as we left, other agents began to show up to search the grounds for any evidence we might of missed.

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**So uhhm yeah... xD I hope that made sense. Sorry again for any grammar/ spelling errors I might of missed.**

**Please Review/Fave and tell me what you think happened to Tony!**

**Thanks for reading!**

**I'll be sure to update again soon!**

**xxx**


	3. Chapter 3

**AUTHORS NOTE: Hey there! First I'd like to thank you all again for reading this story! It really means alot to me! Now back to the reason you're here _ I'm not overly fond of this Chapter but I hope you guys like it ~ I assure you things are going to get better and alot more interesting!**

**I'm also gonna go ahead and warn you: There's a bit of bad language in this chapter ... But nothing to serious.**

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**Chapter 3: **Assembled.

_Nick Fury's POV_

A few hours passed before the team was assembled, everyone except for Thor and of course Tony was there. I walked into the room where the remaining Avengers were seated. The room was quiet, you wouldn't expect four superheroes to be so... Speechless.

I took my seat at the table and motioned for them to listen. They all shifted their gaze towards me.

"I suppose all of you know why you're here."I said out loud and all of them nodded slowly.

The room fell silent once more before Steve decided to break it.

"Fury... Can you give us any details? What exactly happened?"He asked getting everyone's attention.

I bit my lip."Well, that's the problem captain... We have no idea."I replied with a audible sigh."We haven't had any reports of witnesses or anything that can help us. I was actually on the phone with Stark when it happened. He was talking to me one second and the next there was a deafening sound, then his suit collided with _something_ and the line went dead."

Bruce dropped his head into his hands. "So we have absolutely no leads?"

"Unfortunately not."I added and Steve jumped up.

"Look we have to do something! Stark might be an ass on occations but he's still part of the team! He could be dying at this very moment and what are we doing? Sitting here!"He exclaimed and hit the table with his fist.

Barton and I both sighed in unison."Captain calm down! There's not much we can do right now! We have no leads! Which means we have no idea where to start looking for him! The only thing we can do now is wait and trust we'll get something to work with soon..." Barton clarified. "All of us are worried about him... He's a friend and a member of our team and we won't just give up on him but we can't afford to go on wild-goose chase right no-"

The door swung open with a loud crash leaving Barton's sentence unfinished.

"Friends! I bring terrible news!"Thor's voice suddenly echoed through the room causing everyone to nearly jump out of their skin.

"Thor?" I asked confused and the rest of the Avengers turned to face him.

"What the hell was that all about Tho-" Natasha asked but got interrupted.

"That is not of importance right now! I have crucial news..." Thor repeated slightly annoyed.

"We're listening."I said and motioned for him to continue.

Thor gathered his breath before he met my eyes with his. "It's my brother. He escaped prison at dawn. There has been no trace of him ever since but we fear he might of left the realm of Asgard." He paused and shifted his gaze to the ground."And the only other place my brothers has access to that I know of is Midgard."

I huffed and turned to face the door."Well everyone. I guess we know who has Stark now." I stated and began to walk.

"What happened to the man of iron?"Thor questioned.

"You should ask your brother that Thor." I answered and stopped."Everyone I need you to do whatever you can to track down the possible location of Loki. Hell. Do what we did last time, catch that son of a bitch on camera."I ordered with a grin that faded away shortly after."Also Agent Romanoff I think it might be time to let Mrs. Stark know... We can't keep this a secret from her any longer, she's expecting him home soon... I'm going to need your help on this."I added and walked out the door.

"Yes sir."Natasha called out and followed me.

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**I'm really sorry for the short chapter but like I mentioned earlier... not my best work -_- ... I hope you enjoyed it though! Please Review/Follow and I'll be sure to upload another chapter as soon as possible! :D**

**Thanks for reading!**

**xxx**


	4. Chapter 4

**Authors Note: ****Well... I- I can explain... Omgosh I am so sorry for not updating in- uh... 3 or 4 months. Life has been pretty interesting and busy... I've moved, written exams and a list of other things but I'm not going to get into that to much... ANYWAYS... Again I'm sososo sorry but rather late than never right? RIGHT? :D**

**I'd like to thank you all for the lovely reviews/favorites/follows so far and I hope you enjoy this chapter.**

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**Chapter 4:**

_Pepper's POV_

I sat in the living room, I had just finished preparing dinner for two. Tony was going to be home any minute now and I couldn't wait to share the news about my pregnancy with him! I'm not sure how he's going to react though, we've never really talked about having kids but whats done is done...Honestly, I was actually really looking forward to it.

I raised my right eyebrow slightly when I heard the door bell ring. I wasn't expecting any company other than Tony and I'm sure he would of used the entery in his workshop.

"Jarvis, who is at the door?"I asked in a whisper.

"It appears to be Nick Fury and Agent Romanoff, Mrs. Stark." The Al responded shortly after.

I felt my stomach turn. Why would they be here instead of Tony? I walked over to the door slowly... My heart was racing in my chest. I knew something was wrong.

I opened the door and both of them met my worried eyes. "Mrs. Stark can we come in?" Nick Fury asked earnestly.

I motioned for them to enter, we walked to the livingroom before he finally spoke again. "Mrs. Stark-"

"Please, call me Pepper."I interupted him.

"Okay, Pepper. We have some serious news about Tony."He added with a sympathetic look.

I felt my knees go weak."W-what is it? Is he okay?"I asked. I could feel tears stinging the back of my eyes. Silence filled the room once more as they tried to find their words. It was driving me crazy. "JUST TELL ME!" I shouted at the top of my lungs as tears began to run down my cheeks. I couldn't take not knowing anymore...

Natasha cleared her throat awkwardly. " Pepper... Tony was kidnapped earlier today, we're not sure whether he's alive or not, but we're assuming he is... We suspect Loki was the one who kidnapped him but I promise you we're doing everything we can to find him..."She whispered and gave me all the details they had on what happened.

I bit my lip as my knees finally gave out under me, I managed to land on the couch that I was conviniantly standing infront of. "No...nonononono, this can't be happening."I whispered and rested my head in my hands. "Please tell me you're kidding!"

"I'm sorry, I wish I was."Natasha whisped back. "Pepper, we'll get him back for you... I promise." she added and sat down next to me, she gave Fury a look telling him 'she'll try and handle things from there.' He nodded and dismissed himself from the room.

How could all of this happen now and why to Tony? I wept silently. "You know what N-Natasha?"I sniffed wiping away some tears.

"No, what?"She asked softly.

"This is the worst possible time for this to happen, not that it would _ever_ be a good thing but-"I said and felt my voice crack,"I was going to tell Tony tha-that I'm pregnant when he got back- and now, he might never know." I whispered and felt the tears start to roll down my face again.

Natasha's eyes widened slightly but also softened before she gave me a gentle hug. "Pepper I-"She whispered unable to find the right words. "Don't think like that, alright?"

"I'll try."I whispered and wept into her shoulder. I wanted my Tony back...I wanted him back right now. I wanted him to hold me and never let go; and most of all I wanted him to know that he was going to be a daddy, and a brilliant one in fact.

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_Tony's POV_

I opened my eyes slowly. Nothing but darkness surrounded me. I tried taking a deep breath but just ended up coughing... "W-what?" I whispered but I couldn't even recognize my own voice. My entire body felt sore, yet I couldn't quite remember why. I tried pulling myself to my feet but found my hands were tied up. I pulled at the ropes but I didn't have enough strength to try and escape at that very moment.

Just as I wanted to shut my eyes again, I heard a huge iron door crack open a few meters away and seconds later, the bright lights almost blinded me. My eyes took a while to ajust but when I was finally able to see again, a very familiar figure stood infront of me.

"Well."I paused slightly shocked."Aren't _you_ suppose to be in prison somewhere?" I asked curiously but he just grinned down at me.

I rolled my eyes after getting no responce. "Fine, would you atleast be kind enough and enlighten we on why I'm here?" I coughed and he came closer. Till we were face to face.

"Oh you'll find out soon enough **Stark**."Loki replied calmly before he turned around and went back the way he came from. "I'll be back to check up on you in a few _short_ hours... Then, and only then we'll start with our little project."He smirked and began to shut the door. "Don't do anything stupid in the meantime." He added as the door finally closed and I was left alone again.

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**Whoo! Please review/follow if you like it and I'll be sure to get another chapter up here as soon as I can...**

**Thanks for reading!**

**xxx**

**-TC**


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